The Australian singer's hit was featured on the April 10 episode of the Fox show, where it was performed by series star Darren Criss and White Collar's Matt Bomer.
"They did such a faithful arrangement of the instruments but the vocals were that pop Glee style, ultra dry, sounded pretty tuned and the rock has no real sense, like it's playing to you from a cardboard box," Gotye told The Sunday Mail.
"It made it sound dinky and wrong," he continued.
Gotye performed the hit song on Saturday Night Live on April 14.
Glee airs Tuesdays at 8/7c on Fox in the US and Thursdays at 9pm on Sky1 in the UK.
Watch Glee's cover of 'Somebody That I Used to Know' below: